tbuckley/cabot-search huggingface dataset:
Abstract 604: Hybrid quantification of SILAC-barcoded interacting tumor and T cells
Authors: Sofía Ibáñez Molero, Alisha Atmopawiro, Alex Terry, Maarten Altelaar, Daniel Peeper, Kelly Stecker
Journal: Cancer Research (2023)

Abstract Therapeutic interference of cell-cell communication mechanisms has allowed the clinical development of multiple cancer treatments. For example, the therapeutic intervention of T cell-tumor cell interactions of PD-1 and PD-L1, respectively, by immune checkpoint blockade (ICB) has improved the clinical outcome of cancer patients. However, only a minority of patients are currently benefiting from ICB. Thus, there is an urgent need to improve our understanding of the T cell-tumor cell interplay. Recently developed algorithms serve to deconvolute gene expression of physically interacting cells (PIC). However, such approaches are limited for proteomics (MS) and phosphoproteomics (pMS), which are required to get molecular insight into protein functionality. Here, we present a new method: Hybrid quantification of SILAC-barcoded interacting cells (HySic). Briefly, we use Stable Isotope Labelling by Amino acids in Cell culture (SILAC) to differentiate between two cell types of interest: T cells and tumor cells. We co-cultured the cells allowing to engage in functional interactions and without the need to separate them, and subsequently performed a label-free quantification (LFQ) LC-MS analysis. After initial bioinformatic analysis and validation with independent techniques, we used HySic to unravel protein mechanisms contributing to functional T cell-tumor cell interactions. We used established interaction mechanisms like those mediated by IFNγ signaling proteins to benchmark HySic, while this analysis also brought new protein pathways to light, which will be presented. In conclusion, we have established and validated HySIC as a new method to study protein signaling dynamics in physically interacting cells. Our data shows the effectiveness and applicability of HySIC to study cell-cell interactions, which could be easily extended to other biological systems. Citation Format: Sofía Ibáñez Molero, Alisha Atmopawiro, Alex Terry, Maarten Altelaar, Daniel Peeper, Kelly Stecker. Hybrid quantification of SILAC-barcoded interacting tumor and T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 604.
Abstract 4691: Spatially resolved transcriptomics deconvolutes histological prognostic subgroups in patients with colorectal cancer and synchronous liver metastases
Authors: Colin S. Wood, Kathryn A. Pennel, Holly Leslie, Assya Legrini, Andrew J. Cameron, Paul Horgan, Joanne Edwards, Colin W. Steele, Nigel B. Jamieson
Journal: Cancer Research (2023)

Abstract Patients demonstrating strong immune responses to primary colorectal cancer (CRC) have a survival benefit following surgery, while those with predominantly stromal microenvironments do poorly. Biomarkers to identify patients with colorectal cancer liver metastases (CRLM) who have good prognosis following surgery for oligometastatic disease remain elusive. The aim of this study was to determine the practical application of a simple histological assessment of immune cell infiltration and stromal content in predicting outcome following synchronous resection of primary CRC and CRLM, and to interrogate the underlying functional biology that drives disease progression. Patients undergoing synchronous resection of primary CRC and CRLM underwent detailed histological assessment, panel genomic and bulk transcriptomic assessment, immunohistochemistry (IHC) and GeoMx Spatial Transcriptomics (ST) analysis. Integration with genomic features, pathway enrichment analysis and immune deconvolution were performed. High-immune metastases were associated with improved cancer specific survival (HR, 0.36, P=0.01). Bulk transcriptomic analysis was confounded by stromal content but ST demonstrated that the invasive edge of the metastases of long-term survivors was characterized by adaptive immune cell populations enriched for Type II Interferon signaling (NES=-2.05 P.Adj&amp;lt;0.005) and MHC-Class II Antigen Presentation (NES=-2.09 P.Adj&amp;lt;0.005). In contrast, patients with poor prognosis demonstrated increased abundance of regulatory T-cells and neutrophils with enrichment of Notch (NES=2.2 P.Adj=0.022) and TGF-β (NES=2.2 P.Adj=0.02) signaling pathways at the metastatic tumor center. In summary, histological assessment can stratify outcome in patients undergoing synchronous resection of CRLM and ST analysis has revealed significant intra-tumoral and inter-lesional heterogeneity with underlying transcriptomic programs identified in driving each phenotype. Citation Format: Colin S. Wood, Kathryn A. Pennel, Holly Leslie, Assya Legrini, Andrew J. Cameron, Paul Horgan, Joanne Edwards, Colin W. Steele, Nigel B. Jamieson. Spatially resolved transcriptomics deconvolutes histological prognostic subgroups in patients with colorectal cancer and synchronous liver metastases. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4691.
Abstract 3046: Association of XRCC1 Arg194Trp polymorphism and XPD Lys751Gln polymorphism with biochemical parameters, severity and risk of prostate cancer in Bangladesh Population
Authors: Nafisa Ahmed, MD. Ariful Islam, M. Mahboob Hossain, Yearul Kabir
Journal: Cancer Research (2023)

Abstract a)To evaluate the association between x-ray cross-complementing gene 1 (XRCC1) polymorphism Arg194Gln and xeroderma pigmentosum group D (XPD) polymorphism Lys751Gln with severity and risk of prostate cancer as well as with biochemical parameters of prostate cancer patients in Bangladesh population. b) Blood samples and data were collected from 132 prostate cancer patients and 135 healthy controls among Bangladesh population. Genotype analysis was done by the PCR-RFLP method. Statistical analysis was performed using GraphPad Prism 9.4.1 software. c) Only the recessive model, that is, carrying two copies of the XRCC1 194 codon Trp allele was positively associated with prostate cancer, with an OR of 7.50 (95% CI, 1.227-85.12; p=0.035). No association was found between the XPD variants with prostate cancer risk. Keeping the wild type and heterozygous genotype as a reference, the combined effects of the XRCC1 codon 194 Arg/Arg and the XPD codon 751 Gln/Gln genotype were found to be significantly associated with prostate cancer risk with an OR of 3.25 (95% CI, 1.39-8.20; p=0.006). XRCC1 194 Trp/Trp genotype was significantly associated with obstructive features, such as hematuria and creatinine levels of the prostate cancer patients (P&amp;lt;0.05). Moreover, the homozygous mutant Gln/Gln genotype of XPD gene was also significantly associated with creatinine levels in prostate cancer patients. No association was found between any of the variants of XRCC1 and XPD with invasiveness, tumor grade, prostate ultrasound scan results, digital rectal examination, Urine R/E or Prostate Specific Antigen (PSA) results (P&amp;gt;0.05). d) Only the XRCC1 codon 194 Trp allele showed a modest association with prostate cancer risk with an 8.19-fold increased risk when two copies of the allele were present. When both alleles- XRCC1 codon 194 and XPD codon 751 Gln -were present in their homozygous states, the risk for prostate cancer increased by 3.2-folds. Our results showed a significant association between XRCC1 194 Trp/Trp with obstructive features and and levels of creatinine in prostate cancer patients of Bangladeshi men. Citation Format: Nafisa Ahmed, MD. Ariful Islam, M. Mahboob Hossain, Yearul Kabir. Association of XRCC1 Arg194Trp polymorphism and XPD Lys751Gln polymorphism with biochemical parameters, severity and risk of prostate cancer in Bangladesh Population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3046.
Abstract 5898: Gut microbiota-derived metabolism of 5-fluorouracil affects drug efficacy
Authors: Despoina Chrysostomou, Mark David, James L. Alexander, Julian R. Marchesi, James M. Kinross
Journal: Cancer Research (2023)

Abstract Introduction: Fluoropyrimidines are drugs currently used as a first-line treatment for colorectal cancer (CRC)1. The impact of gut bacteria on 5-Fluorouracil (5FU) activity remains relatively unknown. The objective of this analysis was to delineate potential bacteria-drug interactions that modify 5FU. Methods: Tumor and tumor-adjacent healthy tissue samples from 130 colorectal adenocarcinoma patients, 55% males and 45% females, median age of 71 years old (36-91 age range), were extracted following surgical resection of the tumor. TNM classification varied across the cohort (15% pT1, 43% pT2, 35% pT3, 4% pT4). 16s rRNA gene amplicon sequencing was performed to map the microbiome composition of tumor and paired normal mucosa. 20 bacterial from the genera whose abundance changed significantly between tumor and healthy tissue were incubated with 5FU to assess drug-bacteria interactions. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was employed to identify changes in drug concentration (Wilcoxon spare rank test) as well as products of bacteria-driven drug metabolism. A metabolic activity-based assay was used to assess viability of a colorectal adenocarcinoma cell line (HCA46) following co-incubation with microbe-driven drug metabolites, aiming to determine significant effects on 5FU efficacy, assessed by 2-way ANOVA. Results: Escherichia coli BW25113, Bifidobacterium longum, Citrobacter freundii and Enterococcus faecalis significantly modify 5FU in vitro, allowing us to conclude that bacteria can metabolise the drug (q &amp;lt; 0.001). Ruminococcus gnavus does not have the ability to metabolise the drug as no significant change in 5FU concentration was observed. Incubation of microbe-derived drug metabolites with HCA46 resulted in significant decrease in cell viability compared to incubation with 5FU only, indicating that bacteria-5FU interactions result in increase of drug efficacy (Figure 2). Conclusion: This is the first report of 5FU metabolism by Escherichia coli BW25113, Bifidobacterium longum, Citrobacter freundii and Enterococcus faecalis in vitro. This study provides an insight into the potential of large and small intestinal bacteria in chemically modifying chemotherapeutic agents and therefore modulating their activity. 1. Mahipal A, Grothey A. Role of biologics in first-line treatment of colorectal cancer. J Oncol Pract. 2016. Citation Format: Despoina Chrysostomou, Mark David, James L. Alexander, Julian R. Marchesi, James M. Kinross. Gut microbiota-derived metabolism of 5-fluorouracil affects drug efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5898.
Abstract 5895: Analysis of microbiome in gastric MALT lymphoma
Authors: SeungJoo Yoo, Dong-Yeop Shin, Ja Min Byun, Junshik Hong, Hongseok Yun, Youngil Koh, Sung-Soo Yoon
Journal: Cancer Research (2023)

Abstract Gastric MALT (mucosa-associated lymphoid tissue) lymphoma is found at a rate of 50% or more among the types of MALT lymphoma. Majority of patients with gastric MALT lymphoma are infected with Helicobacter pylori and also have clinical improvement with eradication therapy. However, it is unclear how H. pylori cause gastric MALT lymphoma. To explore it, we prospectively collected 13 patients who are newly diagnosed with gastric MALT lymphoma with H. pylori. We gathered samples from normal regions and lesions during endoscopy for diagnosis. Samples of lesion were harvested again after eradication of H. pylori. we sequenced 10 of WES (whole exome sequencing) and 13 of WTS (whole transcriptome sequencing) with these samples. With sequencing data, we aligned the sequenced reads to human reference genome (hg19) using BWA and called the variants with Mutect2. We aligned the reads and calculated TPM (Transcripts Per Million) from WTS with STAR and RSEM. We performed DEG (Differentially Expressed Genes) and GSEA (Gene Set Enrichment Analysis) for three comparison groups which are divided into normal, lesion, and after eradication. Gene fusions were detected using STAR-Fusion and Arriba with WTS. To detect potential microbiome from the samples, we used Kraken2, a taxonomic classification tool. We found that MUC6 was mutated from all samples and some samples have mutated MUC3A, KMT2C, ZNF595, CDC27, etc., and two have BIRC3-MALT1 fusion. From DEG and GSEA analysis, G protein-coupled receptor activity was activated in the group of lesion samples and suppressed in normal samples and eradication samples. Lymphocyte activation and immune response were also activated in the cancerous lesion. Kraken2 classified the reads which were not aligned to the human reference genome as reads from microbiota including H. pylori. The reads of H. pylori were more abundant in the lesion group than the other groups. According to the result of differentially expressed species analysis between the groups of lesion and eradication, the following species were also more abundant in the lesion group; Veillonella dispar, Helicobacter hepaticus, Helicobacter winghamensis, etc. We analyzed genetic alterations and differentially expressed genes and also classified non-human reads as microbiome with sequencing data from gastric MALT lymphoma. Our results suggest how H.pylori infection is related to carcinogenesis of gastric MALT lymphoma. Citation Format: SeungJoo Yoo, Dong-Yeop Shin, Ja Min Byun, Junshik Hong, Hongseok Yun, Youngil Koh, Sung-Soo Yoon. Analysis of microbiome in gastric MALT lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5895.
Abstract 1876: NAV-001, a high-efficacy antibody-drug conjugate targeting mesothelin with improved delivery of potent payload by counteracting MUC16/CA125 effects
Authors: Luigi Grasso, J. Bradford Kline, Nicholas C. Nicolaides
Journal: Cancer Research (2023)

Abstract Subsets of tumor-produced proteins, referred to as Humoral Immuno-Oncology (HIO) factors, can bind to IgG1 antibodies and suppress their immune-effector activities. Antibody-drug conjugates (ADCs) targeting tumor cell surface antigens can internalize and kill target cells upon liberation of their cytotoxic payload. Binding of the antibody component of an ADC by a HIO factor may potentially hamper the efficacy of a bound ADC. To assess any suppression of ADC’s activity by HIO factors, we evaluated the efficacy of a HIO-refractory ADC, NAV-001, and a HIO-bound ADC, SS1, both targeting mesothelin. The HIO factor MUC16/CA125 protein, which binds to SS1 ADC, was shown to have a negative effect on its internalization and tumor cell killing. The MUC16/CA125 refractory NAV-001 ADC was shown to have robust killing of tumor cells regardless of MUC16/CA125 expression in vitro (EC50 ~20 pM) as well as in vivo at single, sub-mg/kg dosing. Moreover, NAV-001-PNU, which contains the PNU-159682 topoisomerase II inhibitor as a payload, demonstrated good stability in vitro and in vivo as well as robust bystander activity against tumor and stromal cells not expressing the target antigen mesothelin, while maintaining a tolerable safety profile in vivo. Single-dose NAV-001-PNU demonstrated robust tumor regression of a number of patient-derived xenograft models from different tumor types regardless of MUC16/CA125 expression. These findings suggest that identification of HIO-refractory antibodies to be used in ADC format may improve therapeutic efficacy as observed for NAV-001 and warrants NAV-001-PNU’s advancement to human clinical trials as a monotherapy to treat mesothelin-positive cancers. Citation Format: Luigi Grasso, J. Bradford Kline, Nicholas C. Nicolaides. NAV-001, a high-efficacy antibody-drug conjugate targeting mesothelin with improved delivery of potent payload by counteracting MUC16/CA125 effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1876.
Abstract 3753: miR-567 modulates the progression of melanoma cells and functions of macrophages
Authors: Mai-Huong Thi Nguyen, Chen-Huan Lin, Yu-Chi Huang, Mu-Shiun Tsai, Ming-Hong Chen, Azusa Miyashita, Satoshi Fukushima, Nianhan Ma
Journal: Cancer Research (2023)

Abstract Purpose: Target therapy and immunotherapy are advancements in the treatment of melanoma; unfortunately, a subset of patients does not benefit or produces drug resistance. Therefore, an alternative strategy should be investigated to further improve clinical benefits. Macrophages are the abundant immune cells related to the progression of melanoma and resistance to drugs. In this study, we explored the novel roles of miR-567 in the progression of melanoma and effects of macrophages. Methods: miR-567 expression in nevus and melanoma tissues was analyzed by in situ hybridization. miR-567 was transfected into melanoma cells to investigate its biological effects through functional assays such as proliferation, colony formation, soft agar, and migration assays. In addition, miR-567-related signal transduction pathways in the melanoma cells were studied by western blot and next-generation sequencing analyses. Different phenotypes of macrophages polarized from THP-1 monocyte cells were used as in vitro model to investigate the effects of miR-567 on macrophages. Results: Our results showed that miR-567 expression levels were decreased in melanoma cells compared to melanocyte cells. Consistently, expression of miR-567 was 0.403-fold lower in melanoma tissues (n=118) as compared to nevus tissues (n=40). In addition, the receiver operating characteristic presented that the area under the curve value of miR-567 is 0.9495. Importantly, higher expression of miR-567 enhanced the overall survival of melanoma patients. Overexpression of miR-567 significantly reduced proliferation, survival, anchorage-independent growth, migratory, and invasive abilities of melanoma cells and BRAF-inhibitor resistant cells. Furthermore, our results demonstrated that IGF1R, E2F1, and Cyclin B2 are direct targets of miR-567 and knockdown of these genes attenuated proliferation and survival of melanoma cells. Interestingly, introduction of miR-567 downregulated MAPK/ERK and PI3K/AKT pathways in melanoma cells and regulated multiple pathways related to immune response. Of note, overexpression of miR-567 reduced the promoting melanoma growth induced by M2 or melanoma-associated macrophages, indicating the involvement of miR-567 in regulation of macrophages. Conclusion: miR-567 could be served not only as biomarkers but also as potential molecular target for prevention of melanoma progression. Citation Format: Mai-Huong Thi Nguyen, Chen-Huan Lin, Yu-Chi Huang, Mu-Shiun Tsai, Ming-Hong Chen, Azusa Miyashita, Satoshi Fukushima, Nianhan Ma. miR-567 modulates the progression of melanoma cells and functions of macrophages. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3753.
Abstract 1256: Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma
Authors: Signe Caksa, Nicole A. Wilski, Erica L. Kitterman, McKenna Q. Glasheen, Jacob S. Heilizer, Timothy J. Purwin, Claudia Capparelli, Andrew E. Aplin
Journal: Cancer Research (2023)

Abstract Cutaneous melanoma is the most fatal skin cancer; resistance to targeted therapies contributes to poor prognosis. In some cases, resistance arises from pre-existing tumor heterogeneity, which allows subpopulations of drug-tolerant cells with distinct transcriptional states to survive in the presence of drug. The loss of SOX10, a lineage-specific transcription factor, is known to drive melanoma phenotype switching from a proliferative to an invasive drug-tolerant state. Here, we found that knocking out SOX10 in human and mouse melanoma cell lines leads to the upregulation of transglutaminase-2 (TGM2), a calcium-dependent cross-linking enzyme. Analysis of publicly available bulk and single-cell RNA-sequencing data showed that TGM2 is highly expressed in the invasive cell state in melanoma cell lines and patient-derived melanoma cultures, respectively. Furthermore, knockdown of SOX10 in patient-derived melanoma cultures increases TGM2 mRNA expression. 3D spheroid assays and extracellular matrix production/remodeling assays showed that knockdown of TGM2 has no effect on the invasiveness of SOX10-deficient cells. However, we found that TGM2 is secreted by SOX10-deficient cells and hypothesized that it could modulate the tumor immune microenvironment (TIME) given that TGM2 has been associated with increased immune infiltration in melanoma patient samples. To investigate the effect of TGM2 on the TIME, we stably overexpressed TGM2/Tgm2 in syngeneic mouse melanoma cell lines and allowed tumors to grow in immune-competent C57BL/6 mice. As compared to empty vector, TGM2/Tgm2-overexpression led to an increase in the percentage and number of CD4+ T cells and B cells, and a decrease in the number of myeloid cells, in the tumor immune compartment by flow cytometry analysis. Future studies will assess which subsets of CD4+ T cells and B cells infiltrate TGM2/Tgm2-overexpressing tumors, how these changes to the TIME affect melanoma invasiveness, and if TGM2 expression affects response to targeted therapy in vivo. Overall, our data suggest that TGM2 is highly expressed in the invasive melanoma cell state, is regulated by the SOX10 transcription factor, and can modulate adaptive immune cells in the TIME. Citation Format: Signe Caksa, Nicole A. Wilski, Erica L. Kitterman, McKenna Q. Glasheen, Jacob S. Heilizer, Timothy J. Purwin, Claudia Capparelli, Andrew E. Aplin. Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1256.